FIX: Auto-detect non-linear frame spacing in MSD._conclude()

Previously, `_conclude()` only used `_conclude_non_linear()` if the user
explicitly set `non_linear=True`. Now it also checks whether the time
intervals between frames are non-uniform (e.g. when passing
`frames=[0, 1, 3, 6]`) and automatically falls back to the non-linear
path, preventing incorrect MSD results from unevenly-spaced trajectories.

Author: spyke7

package/CHANGELOG

@@ -22,6 +22,8 @@ The rules for this file:
  * 2.11.0
 
 Fixes
+ * Fixes msd for non-linear frames, when non_linear is not explicitly
+   provided (Issue #5100, PR #5254)
  * Fixes TypeError with np.int64 indexing in GSD Reader (Issue #5224)
  * Fixed bug in add_transformations allowing non-callable transformations
    (Issue #2558, PR #2558)

package/MDAnalysis/analysis/msd.py

@@ -427,7 +427,12 @@ def _single_frame(self):
         ]
 
     def _conclude(self):
-        if self.non_linear:
+        delta_time = np.diff(self.times)
+
+        if self.non_linear or (
+            len(delta_time) > 1
+            and not (np.allclose(delta_time, delta_time[0]))
+        ):
             self._conclude_non_linear()
         else:
             if self.fft:

testsuite/MDAnalysisTests/analysis/test_msd.py

@@ -1848,3 +1848,18 @@ def test_start_stop_step(self, u_nonlinear):
         assert_allclose(
             result_msd_per_particle, expected_msd_per_particle, rtol=1e-5
         )
+
+    def test_detect_non_linear_from_frames(self, step_traj):
+        msd_auto = MSD(step_traj, select="all", msd_type="xyz", fft=False)
+        res1 = msd_auto.run(frames=[0, 1, 3, 6])
+
+        msd_explicit = MSD(
+            step_traj, select="all", msd_type="xyz", non_linear=True
+        )
+        res2 = msd_explicit.run(frames=[0, 1, 3, 6])
+
+        assert_allclose(
+            res1.results.msds_by_particle,
+            res2.results.msds_by_particle,
+            rtol=1e-5,
+        )